From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Tue May 08 2007 - 16:46:29 CDT
New to the list and considering to download namd,
first I need information that I found difficult to get
from the web site or archive list:
1) Do Parameters come with namd download or should
they be obtained elsewhere? In particular, how to get
the latest CHARMM (or other) parameters as a starting
point?
2) Where to obtain the list of CHARMM (or other) atoms
to be used?
3) Is any tool provided to build Parameters for any
type of functionalities? Can I use my quantum
mechanical code to make them in the frame of such
tool, if any?
4) How are Partial Charges obtained? Can I use those
provided by my quantum mechanical code?
It should be apparent from my questions that I intend
to use namd for interplay of proteins with organic
compounds of wide variety, thus the code should
perform not for proteins or DNA/RNA only. This is also
why I mentioned CHARMM and nor AMBER.
Huge thanks for directing me to where such information
can be found.
francesco pietra
__________________________________________________
Do You Yahoo!?
Tired of spam? Yahoo! Mail has the best spam protection around
http://mail.yahoo.com
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:44:39 CST